If memory serves, they X-Files about 3 seasons in and negotiating (or renegotiating) contracts. Duchovny had successfully lobbied for N amount of money, but when Gillian was trying for the same amount of money, Duchovny balked at supporting her bid with any kind of solidarity. With the way contracts in Hollywood work, who knows if he was being selfish or sensible? But Gillian apparently took this to mean that he valued her contribution to the series less than his own.
Oh, you know he hit that.
I dunno. Duchovny seems kind of snobby about his big big brain, big degree, and acting pedigree, while Anderson comes off as only marginally considerate of others and of fairly average intelligence. He may have considered her beneath him. Or maybe he did hit it, and that made his unwillingness to help her out that much more bitter.
/meaninglessspeculation